Standard Amino Acids of Proteins

TABLE 4-1 Covalent Structures and Abbreviations of the “Standard” Amino Acids of Proteins, Their Occurrence, and the pK Values of Their Ionizable Groups Name, Three-letter Symbol, and One-letter Symbol Residue Mass (D)b Average Occurrence in Proteins (%)c 57.0 7.1 2.35 9.78 71.1 8.2 2.35 9.87 99.1 6.9 2.29 9.74 113.2 9.7 2.33 9.74 113.2 6.0 2.32 9.76 131.2 2.4 2.13 9.28 H2 COO– C3 CH 4 2 C2 5 +1 N CH2 H H2 97.1 4.7 1.95 10.64 COO – 147.2 3.9 2.20 9.31 186.2 1.1 2.46 9.41 Structural Formulaa pK1 𝛂-COOHd pK2 𝛂-NH3+d pKR Side Chaind Amino acids with nonpolar side chains Glycine Gly G COO – H H C NH3+ Alanine Ala A COO – H C CH3 NH3+ Valine Val V COO – CH H 3 CH NH+ CH3 C 3 Leucine Leu L COO – H CH3 C CH2 CH CH3 NH+ 3 Isoleucine Ile I Methionine Met M H COO – CH3 C C* CH2 CH3 NH3+ H COO – H C CH2 CH2 S CH3 NH3+ Proline Pro P Phenylalanine Phe F H C CH2 NH3+ Tryptophan Trp W COO – H C CH2 NH3+ a 4 5 3 2 1 N H 6 7 The ionic forms shown are those predominating at pH 7.0 (except for that of histidine f ) although residue mass is given for the neutral compound. The Cα atoms, as well as atoms marked with an asterisk, are chiral centers with configurations as indicated according to Fischer projection formulas (Section 4-2). The standard organic numbering system is provided for heterocycles. b The residue masses are given for the neutral residues. For the molecular masses of the parent amino acids, add 18.0 D, the molecular mass of H2O, to the residue masses. For side chain masses, subtract 56.0 D, the formula mass of a peptide group, from the residue masses. c The average amino acid composition in the complete SWISS-PROT database (http://www.expasy.ch/sprot/relnotes/relstat.html), Release 2013_13. Individual proteins may exhibit large deviations from these quantities. d Data from Dawson, R.M.C, Elliott, D.C., Elliott, W.H., and Jones, K.M., Data for Biochemical Research (3rd ed.), pp. 1–31, Oxford Science Publications (1986). TABLE 4-1 (Continued) Name, Three-letter Symbol, and One-letter Symbol Structural Formulaa Amino acids with uncharged polar side chains Serine COO – Ser H C CH2 OH S Residue Mass (D)b Average Occurrence in Proteins (%)c pK1 𝛂-COOHd pK 2 𝛂-NH3+d 87.1 6.6 2.19 9.21 101.1 5.3 2.09 9.10 114.1 4.1 2.14 8.72 128.1 3.9 2.17 9.13 163.2 2.9 2.20 9.21 10.46 (phenol) 103.1 1.4 1.92 10.70 8.37 (sulfhydryl) 128.2 5.9 2.16 9.06 10.54 (ε-NH+3 ) 156.2 5.5 1.82 8.99 12.48 (guanidino) 137.1 2.3 1.80 9.33 6.04 (imidazole) 115.1 5.4 1.99 9.90 3.90 (β-COOH) 129.1 6.8 2.10 9.47 4.07 (γ-COOH) pK R Side Chaind NH+ 3 Threonine Thr T Asparaginee Asn N COO – H H C C* CH3 NH+ 3 OH COO – H C CH2 O C NH+ 3 Glutaminee Gln Q NH2 COO – H C CH2 O CH2 C NH+ 3 Tyrosine Tyr Y NH2 COO – H C CH2 OH NH+ 3 Cysteine Cys C COO – H C CH2 SH NH+ 3 Amino acids with charged polar side chains Lysine Lys K COO – H CH2 C CH2 CH2 CH2 NH3+ CH2 CH2 NH NH+ 3 Arginine Arg R COO – H CH2 C NH2 NH+2 NH+3 Histidinef His H COO – H C CH2 NH+ 3 Aspartic acide Asp D C CH2 NH+ 3 Glutamic acide Glu E NH+ 2 N H O C O– COO – H C CH2 NH+ 3 e 4 3 5 1 COO – H C O CH2 C O– The three- and one-letter symbols for asparagine or aspartic acid are Asx and B, whereas for glutamine or glutamic acid they are Glx and Z. The one-letter symbol for an undetermined or “nonstandard” amino acid is X. f Both neutral and protonated forms of histidine are present at pH 7.0, since its pKR is close to 7.0.